If you’re planning to use javascript on your WordPress blog or website, there is one function with which you should become intimately familiar. That function is wp_enqueue_script(). It will also be helpful if you do a little bit of research into the wp_deregister_script() function, though, the only official information you’ll find about that function is in the codex information about the wp_enqueue_script() function.

Basically, this function keeps a log of all of the javascript files and libraries you want to use in your theme, makes sure you aren’t duplicating any, and then outputs them in the right order. I would recommend setting the $in_footer parameter to boolean true for all of the scripts you enqueue, as that causes WordPress to add the javascript calls to the footer of your pages rather than putting them in the header. In order to do this, though, you need to make sure that you include the wp_footer() function inside of your theme (preferably just above the closing </body> tag).